Clinical and Genomic Evaluations of a persistent fatal SARS-CoV-2 infection in a Goods syndrome patient: A case report (preprint)

COVID-19 resulted from an infection by SARS-Cov-2 which is the main cause of ADRS in global population from 2019 on. It may contribute to higher rate of death among the patients with immunodeficiency based on recent reports. In addition, Good syndrome (GS) as a result of thymoma removal might cause in some long-lasting microbial infections. We described clinical aspects and viral mutations on a case of GS suffering from COVID-19. A 46-year-old man with fever, general respiratory signs and positive COVID-19 PCR test, with the history of thymoma removal surgery was admitted to Masih Daneshvari Hospital, Tehran, Iran. Lung radiographs and Oxygen saturation measurement disclosed considerable implication resulted in application of several anti-microbial medication. The delta variant (B.1.617.2 (21J Clade)) was the strain isolated from the patient by sequencing methods done by CNRL while the dominant strain circulated mostly among population was Omicron (B.1.1.529) at the time of sampling. Unfortunately, the patient had passed away a month later by sudden respiratory failure progressed in refractory septic shock. Despite the fact that opportunistic infections may lead the GS patients to a major health problematic condition, unusual persistent of infections such as non-dominant variant of SARS-Cov-2 could be observed through the disease timeline. Therefore, a fully screening of thymoma plus intra-host evolution monitoring of SARS-CoV-2 is highly recommended in immunocompromised patients.

Long-standing COVID-19 disease in immunedeficient patients; case reports and literature review (preprint)

Introduction: Patients with primary or secondary immunodeficiency are at higher risk of severe disease and death following SARS-CoV-2 infection compared with the general population. We describe here the effect of rituximab therapy in 5 patients with humoral and cellular immune deficiencies (1 patient with thymoma or Good`syndrome, 1 HIV/AIDS positive patient, 2 patients with Multiple Sclerosis (MS) and 1 patient with chronic lymphocytic leukemia (CLL). T cell responses were evaluated using the QuantiFERON SARS-CoV-2 assay following incubation with the SARS-CoV-2 Ag1, Ag2 and Ag3 viral antigens. Immunephenotyping of T cells (TCD4+, TCD8+) and B cells (CD19+ and CD20+) was determined by flow cytometry. Results: All studied immunocompromised patients showed reduced cellular immune responses (release of interferon (IFN)-g) to SARS-CoV-2 antigens than healthy controls [patients; Ag1, Ag2 and Ag3 and Nil (Median 5-95% percentile) (12 (1-95), 12 (1.5-78), 13.5 (12-95)  and 3 (1-98) U/ml)], ]controls; Ag1,Ag2 and Ag3 and Nil (Median 5-95% percentile) 24.5 (7-89), 65 (31-173), 53.5 (13-71.5) and 3 (1-14) U/ml)]. The frequency of peripheral blood B cells was also reduced in these patients compared to healthy control subjects (p=0.0282). Conclusion: T-cell dependent antibody responses require the activation of B cells by helper T cells. Reduced B cell numbers in immunocompromised patients infected with SARS-CoV-2 indicates the need for these patients to take additional precautions to prevent COVID-19 infection

A case of COVID-19 complicated by Klebsiella pneumoniae, Cytomegalovirus, Aspergillus and Zygomycete infections (preprint)

Co-infection between SARS-CoV-2 and other pathogens have become a serious threat. There are reports of fungal, bacterial and viral co-infections with SARS-COV-2. Herein, we report the unusual case of concomitant aspergillosis, mucormycosis, cytomegalovirus pneumonia and also klebsiella pneumoniae empyema as the complication of COVID-19 infection.

Another step toward final call on Remdesivir efficacy as a treatment for hospitalized COVID-19 patients: a multicenter open-label trial (preprint)

Introduction After emerging the global pandemic of SARS-CoV2 some preliminary studies demonstrated the efficacy of antiviral treatments. But shortly thereafter, inconsistencies in the results of further clinical trials raised doubts on the efficacy of these agents. In this study, we aimed to evaluate the effect of Remdesivir on hospitalized COVID-19 patients’ outcomes. Material and methods This study was an open-label, single-armed, clinical trial on hospitalized patients diagnosed with COVID-19 who had progressive respiratory symptoms despite receiving standard care. All patients received Remdesivir and their characteristics, outcomes, time of treatment initiation, and respiratory support stages during hospitalization were registered and followed up for 14 days. Results 145 patients with the mean age of 52.89 ± 1.12 years enrolled in this study, 38 (26.2%) died at the end of 14 days period. The mean time interval from the onset of the symptoms to antiviral treatment was 10.63±0.56 days. Thirty deceased patients (78.9%) were men, showing 2.8 times higher mortality chance compared to women (OR adj =2.77; 95%CI=1.08-7.09). The type of respiratory support on the first day of treatment initiation showed a significantly lower mortality chance in patients receiving O 2 only than those who needed non-invasive and/or mechanical ventilation (OR adj =3.91; 95%CI=1.64-9.32). The start time (early vs late administration) and duration (less or more than 7 days) of antiviral treatment had no statistically significant association with mortality or ventilation escalation among the patients (p-value > 0.05). Conclusion In this study, we showed that Remdesivir probably is not effective on the outcome of hospitalized COVID-19 patients.

Evaluation of lymphocyte subtypes in COVID-19 patients (preprint)

BackgroundAlthough the many aspects of COVID-19 have not been yet recognized, it seems that the dysregulation of the immune system has a very important role in the progression of the disease. In this study the lymphocyte subsets were evaluated in COVID-19 patients with different severity. MethodsIn this prospective study, the levels of peripheral lymphocyte subsets (CD3+, CD4+, CD8+ T cells; CD19+ and CD20+ B cells; CD16+/CD56+ NK cells, and CD4+/CD25+/FOXP3+ regulatory T cells) were measured in 67 confirmed patients with COVID-19 on the first day of admission. ResultsThe mean age of cases was 51.3 {+/-} 14.8 years. Thirty-two patients (47.8%) were classified as severe cases and 11 (16.4%) patients were categorized as critical. The frequency of blood lymphocytes, CD3+ cells, CD25+FOXP3+ T cells; and absolute count of CD3+ T cells, CD25+FOXP3+ T cells, CD4+ T cells, CD8+ T cells, CD16+56+ lymphocytes were lower in more severe cases in comparison to milder cases. Percentages of lymphocytes, T cells, and NK cells were significantly lower inthe patients who died (p= 0.002 and P= 0.042, p=0.006, respectively). ConclusionFindings of this cohort study suggests that the frequency of CD4+, CD8+, CD25+FOXP3+ T cells, and NK cells were difference in the severe COVID-19 patients. Moreover, lower frequency of, T cells, and NK cells are predictors of mortality of these patients.

SARS-COV-2 Seroprevalence among Health Care Workers in Private and Public Hospitals in Tehran, Iran (preprint)

BackgroundEstimating the prevalence of SARS-COV-2 antibody seropositivity among health care workers (HCWs) is crucial. In this study the seroprevalence of anti-SARS-COV-2 antibodies among HCWs of five hospitals of Tehran-Iran with high COVID-9 patient’s referrals was assessed.MethodsHCWs from public and private hospitals were included and were asked questions on their demographic characteristics, medical history, hospital role and usage of personal protective equipment (PPE). Seroprevalence was estimated on the basis of ELISA test results (IgG and IgM antibodies in blood samples) and adjusted for test performance.ResultsAmong the 2065 participants, 88.4% and 11.6% HCWs were recruited from the public and private hospitals, respectively. The overall test-performance adjusted seroprevalence estimate among HCWs was 22.6 (95% CI 20.2-25.1) and it was higher in private hospitals (37.0%; 95% CI 28.6-46.2) than public hospitals (20.7%; 95% CI 18.2-23.3). PPE usage was significantly higher among HCWs of public versus private hospitals (66.5% vs. 20.0%). Test-adjusted seroprevalence estimates were highest among assistant nurses and nurses, and lowest among janitor/superintendent categories. ConclusionsSeroprevalence of SARS-COV-2 among HCWs depends on hospital type, hospital department, and hospital role. The PPE usage was especially suboptimal among HCWs in private hospitals. Continued effort in access to adequate PPE is warranted.

COVID-19 associated rhinosinusitis mucormycosis due to Rhizopus arrhizus: A rare but potentially fatal infection occurring after treatment with corticosteroids (preprint)

Coronavirus disease 2019 (COVID-19) first emerged in Wuhan, China in December 2019, and since then the frequency of bacterial and fungal coinfections has been continuously rising. While invasive pulmonary aspergillosis is increasingly being recognized in association with COVID-19, there is limited information with regards to COVID-19 associated mucormycosis. Here, we describe a 50-year-old woman with uncontrolled diabetes who received systemic corticosteroids and remdesevir during her admission for COVID-19. Few days after discharge, the patient was readmitted due to facial swelling and numbness, and a diagnosis of COVID-19 associated rhinosinusitis mucormycosis due to Rhizopus arrhizus (formerly Rhizopus oryzae) was confirmed with sequencing of the internal transcribed spacer (ITS) region of the ribosomal DNA. This report aims to address the importance of short-term follow-up in COVID-19 patients who have received systemic corticosteroids, particularly those with predisposing conditions, as early detection and prompt, aggressive treatment is essential for the management of invasive fungal infections.

COVID-19 Antibody Seroprevalence Among General Population and High-Risk Occupational Groups in Eighteen Cities of Iran (preprint)

Background: As the COVID-19 pandemic unfolded, rapid case increase was observed in multiple cities in Iran. However, in the absence of seroprevalence surveys, the true infection rate remains unknown. In this population-based study we assessed the seroprevalence of SARS-CoV-2 antibodies in eighteen cities of Iran.Methods: We randomly selected and invited study participants from the general population (N = 3,547) and occupations with high risk of COVID-19 exposure, defined as high-risk population (e.g., supermarket employees) (N = 5,391), in eighteen cities of Iran. SARS-CoV-2 ELISA kits were used to detect antibody against COVID-19. Crude, population weight adjusted, and test performance adjusted seroprevalence rates were estimated.Findings: The population weight adjusted and test performance adjusted prevalence rates of antibody seropositivity in general population were 13·1% (95% CI 11·6-14·8%) and 18·5% (95% CI 16·1-21·3%), respectively. The population-weighted seroprevalence estimate implies that 3,290,633 (95% CI 2,907185-3,709,167) individuals, from the eighteen included cities in this study, were infected by end of April 2020.The overall prevalence rate was higher among individuals aged ≥ 60 years (32·0%, 95% CI 23·9-40·8%) and with comorbidity condition (23·7%, 95% CI 18·5-28·8%). The estimated seroprevalence of SARS-CoV-2 antibodies varied greatly by city and the highest population test-adjusted prevalence rates were in Rasht 78·1% (95% CI 58·3-98·3%) and Qom (66·5%, 95% CI 39·9-95·4%) cities. The test-adjusted prevalence did not differ between low and high-risk populations and was about 20.0%.Interpretations: The findings of this study imply that prevalence of seropositivity is likely much higher than the reported prevalence rates based on confirmed COVID-19 cases in Iran. Despite the high seroprevalence rates in a few cities, the low overall prevalence estimates indicate that a large proportion of population is still susceptible to the virus. The similar seroprevalence estimates between low and high-risk occupations might be an indicator of inadequate or low adherence to infection control measures among general population.Funding Statement: Iranian Ministry of Health and Medical Education COVID-19 Grant (number 99-1-97-47964).Declaration of Interests: None to disclose.Ethics Approval Statement: Ethics approval for this study was granted by Vice-Chancellor in Research Affairs-Tehran University of Medical Sciences (IR. TUMS.VCR.REC.1399.308)

COVID-19 Re-infection or Relapse? A Retrospective Multi Center Cohort Study From Iran (preprint)

BackgroundMore than one year of emerging COVID 19 infection, no signs of the pandemic remission appear. Returning of symptomatic patients who had a history of recovered COVID-19 disease with a new positive SARS Cov-2 PCR test after several weeks to months of a negative PCR result is one of the novels challenging phenomena during the pandemic. In this study, we determined the clinical and laboratory characteristics of these Iranian patients and discussed possible reasons.METHODWe retrospectively investigated the SARS Cov-2 PCR tests performed in the three referral hospitals six months after the pandemic onset. All patients who had the following criteria were included in the study: two SARS COV2 PCR positive tests three months apart, have no symptoms, and a negative PCR between the two positive tests, access to the patient and his medical information. Then, retrospectively recorded the clinical and laboratory characteristics of the eligible patients. We also compare clinical and laboratory features of the second episode to the first.RESULTA total of 32,567 tests were performed, of which 1899 patients. Finally, 37 cases were eligible in the study based on our criteria. The majority of patients were male and nurses. The mean body mass index was 25.84±3.25. The mean age was 37.54 ±15.16 years old. Weakness, myalgia, and fever were the most clinical presentation symptoms in both episodes. Chest Computed Tomography (CT) scan showed pneumonia in 56.8% and 43.2% of cases in the first and second episodes, respectively. The mean duration between the discharge and second presentation was 117±61.42 days. Seven (18.9%) patients hospitalized in the second episode compared to 2 (5.4%) cases in the first. The clinical, radiological, and laboratory characteristics were not significantly different between the two episodes except for significantly more dexamethasone usage in the second one (p= 0.03).CONCLSIONAlthough we could not perform the phylogenic sequencing of SARS-CoV-2 and viral culture in the re-presenting symptomatic patients with positive RT-PCR, prolonged duration between two episodes suggest probably reinfection in our cases. Finally, this clinical phenomenon may be more common in healthcare providers without a significant consequence.

Decreased neutrophil phagocytosis and killing of bacteria in COVID-19 patients (preprint)

A new coronavirus disease was described in December 2019 (COVID-19) in Wuhan City, Hubei Province, China and has reached pandemic status. According to the World Health Organization, the incubation time from being infected to symptom emergence averages 5-6 days for COVID-19 but can be up to 14 days. The mortality rate varies in different countries but is greater in elderly people and in patients with cardiovascular disease, diabetes and chronic respiratory diseases. Patients with chronic respiratory diseases often have reduced neutrophil function. We sought to measure neutrophil phagocytosis and bacterial killing in COVID-19 patients. 30 COVID-19 patients and 9 healthy individuals were recruited from the Masih Daneshvari Hospital (Tehran, Iran) from March-May 2020. Polymorphonuclear (PMN) cells were isolated from whole fresh blood and incubated with green fluorescent protein (GFP) labelled methicillin-resistant Staphylococcus aureus and Pseudomonas aeruginosa. Phagocytosis was determined by measuring the florescence of co-cultures of bacteria and neutrophils and reported as the lag time before exponential growth. The number of viable bacteria was determined after 70 h by the Colony-Forming Unit (CFU). Bacterial phagocytosis of SA (22±0.9 versus 9.2±0.5h, p<0.01) and PA (12.4±0.6 versus 4.5±0.22, p<0.01) was significantly reduced in COVID-19 patients compared with healthy control subjects. After 70h there was a significant increase in CFU in COVID-19 subjects compared with healthy control subjects for both SA (2.6±0.09 x 108 versus 0.8±0.04 x 108 CFU/ml, p<0.001) and PA (2.2±0.09 x 109 versus 1.0±0.06 x 109 CFU/ml, p<0.001).These results suggests a defect in bacterial clearance by neutrophils in COVID-19 patients.  

Happy Hypoxia: Higher NO in red blood cells of COVID-19 patients (preprint)

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes coronavirus disease 2019 (COVID-19) has spread to almost 100 countries, infected over 10M patients and resulted in 505K deaths worldwide as of 30th June 2020. The major clinical feature of severe COVID-19 requiring ventilation is acute Respiratory Distress Syndrome (ARDS) with multi-functional failure as a result of a cytokine storm with increased serum levels of cytokines. The pathogenesis of the respiratory failure in COVID-19 is yet unknown, but diffuse alveolar damage with interstitial thickening leading to compromised gas exchange is a plausible mechanism. Hypoxia has been seen in the COVID-19 patients however, patients present with a distinct phenotype. Intracellular levels of NO playing important role in the vasodilation of small vessels.Objectives: To elucidate the intracellular levels of NO inside of RBCs in COVID-19 patients compared with that of healthy control subjects.Methods: We recruited 14 COVID-19 infected cases who had pulmonary involvement of their disease, 4 non-COVID-19 healthy controls (without pulmonary involvement and were not hypoxic) and 2 hypoxic non-COVID-19 patients subjects who presented at the Masih Daneshvari Hospital of Tehran, Iran between March-May 2020. Whole blood samples were harvested from patients and intracellular levels of NO in 1 million red blood cells (RBC) was measured by DAF staining using flow cytometry (FACS Calibour, BD, CA, USA).Results: The Mean florescent of intensity for NO was significantly enhanced in COVID-19 patients compared with healthy control subjects (P≤0.05). As a further control for whether hypoxia induced this higher intracellular NO, we evaluated the levels of NO inside RBC of hypoxic patients. No significant differences in NO levels were seen between the hypoxic and non-hypoxic control group.Conclusions: This pilot study demonstrates increased levels of intracellular NO in RBCs from COVID-19 patients. Future studies should examine whether intracellular NO would be increased in large number of COVID-19 patients for usage of possible NO therapy in severe patients. 

Increased serum levels of soluble TNF-α receptor is associated with mortality of ICU COVID-19 patients (preprint)

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes coronavirus disease 2019 (COVID-19) has spread to almost 100 countries, infected over 10M patients and resulted in 505K deaths worldwide as of 30th June 2020. The major clinical feature of severe COVID-19 requiring ventilation is acute Respiratory Distress Syndrome (ARDS) with multi-functional failure as a result of a cytokine storm with increased serum levels of cytokines such as TNF- and IL-6 being reported. TNF- levels are increased during the cytokine storm in very ill patients and soluble receptors for IL-6 and IL-2 are present in the blood of COVID-19 patients, Objectives: To elucidate the involvement of serum levels of soluble TNF-Receptor of severe and mild COVID-19 patients to determine for severity of disease. Method: We recruited 16 severe COVID-19 patients in the ICU on ventilator support and 26 milder COVID-19 patients who were hospitalised but not within the intensive care unit (ICU) between March-May 2020 at the Masih Daneshvari Hospital Tehran, Iran. After harvesting of whole blood the serum was isolated and soluble TNF-Receptor levels measured by ELISA. Results: Serum levels of the usually inhibitory soluble TNF receptor 1 (sTNFaR1) were significantly elevated in severe COVID-19 patients at admission to ICU. High serum levels of sTNFaR1 were associated with mortality of severe COVID-19 patients treated within ICU. Conclusions: This pilot study demonstrates for role of STNF-aR1 receptor in severity of disease. Future studies should examine whether lower levels of systemic sTNFaR1 at admission may indicate a better disease outcome.